To investigate the application of the conductivity mass balance(CMB) method for baseflow separation in small river basins of southern hilly and mountainous areas, the Yong’an Creek Basin in Zhejiang Province was selected as the study area, where a conductivity monitoring network was established to enable long term and stable observations of water conductivity. The correlations between precipitation, runoff, and conductivity as well as their spatial heterogeneity at different rainfall levels were analyzed. The CMB method was then employed to extract baseflow, and the results were compared with those obtained by other baseflow separation methods. Results indicate that the conductivity in the Yong’an Creek Basin shows a trend of first decreasing and then increasing along the main stream, and in terms of temporal distribution, it has a negative correlation with dry and flood seasons. Compared to the traditional digital filtering method, the hydrograph separation program (HYSEP) method, and the baseflow index (BFI) method, the CMB method can effectively identify significant contributions of long term baseflow, and it demonstrates high stability, particularly in addressing severe water quality fluctuations and rainfall dilution effects.